File size is usually the main culprit for long save times. A mesh can be pretty simple with no details but also very high in polycount, which will take longer to save. Remember that a ZBrush Project File saves all tools (and all of their subtools) loaded into a scene. Even if you’re only working on a single tool, you may still be carrying around everything else you’ve loaded. Saving undo history saves the undo history for every single subtool saved in the file, so this can rapidly bloat a scene with many subtools, and I dont recommend doing this casually.
If you don’t feel that file size accounts for the time it’s taking you to save a file, you should contact Pixologic Support.